Strain identifier

BacDive ID: 7576

Type strain: Yes

Species: Paenarthrobacter nicotinovorans

Strain history: CIP <- 2001, JCM <- DSMZ <- H.J. Knackmuss <- K. Decker

NCBI tax ID(s): 29320 (species)

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General

@ref: 191

BacDive-ID: 7576

DSM-Number: 420

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, mesophilic, Gram-positive, rod-shaped

description: Paenarthrobacter nicotinovorans DSM 420 is a facultative anaerobe, mesophilic, Gram-positive bacterium of the family Micrococcaceae.

NCBI tax id

  • NCBI tax id: 29320
  • Matching level: species

strain history

@refhistory
191<- H.-J. Knackmuss <- K. Decker
67770DSM 420 <-- H. J. Knackmuss <-- K. Decker.
121294CIP <- 2001, JCM <- DSMZ <- H.J. Knackmuss <- K. Decker

doi: 10.13145/bacdive7576.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Micrococcaceae
  • genus: Paenarthrobacter
  • species: Paenarthrobacter nicotinovorans
  • full scientific name: Paenarthrobacter nicotinovorans (Kodama et al. 1992) Busse 2016

  • synonyms

    • @ref: 20215
    • synonym: Arthrobacter nicotinovorans

@ref: 191

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Micrococcaceae

genus: Paenarthrobacter

species: Paenarthrobacter nicotinovorans

full scientific name: Paenarthrobacter nicotinovorans (Kodama et al. 1992) Busse 2016

type strain: yes

Morphology

cell morphology

  • @ref: 121294
  • gram stain: positive
  • cell shape: rod-shaped
  • motility: no

colony morphology

@refcolony colorincubation periodmedium usedhemolysis ability
19535Light ivory10-14 daysISP 2
19535Zinc yellow10-14 daysISP 3
19535Ivory10-14 daysISP 4
1953510-14 daysISP 5
19535Golden yellow10-14 daysISP 6
19535Sand yellow10-14 daysISP 7
1212941

multicellular morphology

@refforms multicellular complexmedium name
19535noISP 2
19535noISP 3
19535noISP 4
19535noISP 5
19535noISP 6
19535noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
191CORYNEBACTERIUM AGAR (DSMZ Medium 53)yeshttps://mediadive.dsmz.de/medium/53Name: CORYNEBACTERIUM AGAR (DSMZ Medium 53) Composition: Agar 15.0 g/l Casein peptone 10.0 g/l NaCl 5.0 g/l Glucose 5.0 g/l Yeast extract 5.0 g/l Distilled water
19535ISP 2yesName: ISP 2 / Yeast Malt Agar (5265); 5265 Composition Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.0 Usage: Maintenance and Taxonomy Organisms: All Actinomycetes
19535ISP 3yesName: ISP 3; 5315 Composition Dog oat flakes 20.0 g/l Trace element solution (5314) 2.5 ml/l Agar 18.0 g/l Preparation: Oat flakes are cooked for 20 minutes, trace element solution and agar are added (in the case of non rolled oat flakes the suspension has to bee filtrated). Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.8 Usage: Maintenance and taxonomy (e.g. SEM As liquid medium for metabolite production) Organisms: All Actinomycetes Trace element solution 5314 Name: Trace element solution 5314; 5314 Composition CaCl2 x H2O 3.0 g/l Fe-III-citrate 1.0 g/l MnSO4 0.2 g/l ZnCl2 0.1 g/l CuSO4 x 5 H2O 0.025 g/l Sodium tetra borate 0.2 g/l CoCl2 x 6 H2O 0.004 g/l Sodium molybdate 0.01 g/l Preparation: Use double destillated water. Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Trace element solution for different media Organisms:
19535ISP 4yesName: ISP 4; DSM 547 Solution I: Difco soluble starch, 10.0 g. Make a paste of the starch with a small amount of cold distilled water and bring to a volume of 500 ml. Solution II: CaCO3 2.0 g K2HPO4 (anhydrous) 1.0 g MgSO4 x 7 H2O 1.0 g NaCl 1.0 g (NH4)2SO4 2.0 g Distilled water 500.0 ml Trace salt solution (see below) 1.0 ml The pH should be between 7.0 and 7.4. Do not adjust if it is within this range. Mix solutions I and II together. Add 20.0 g agar. Liquify agar by steaming at 100°C for 10 to 20 min. Trace element solution: FeSO4 x 7 H2O 0.1 g MnCl2 x 4 H2O 0.1 g ZnSO4 x 7 H2O 0.1 g Distilled water 100.0 ml
19535ISP 5yesName: ISP 5 (5323) Composition L-Asparagine 1.0 g/l Glycerol 10.0 g/l K2HPO4 1.0 g/l Salt solution (see preparation) 1.0 ml/l Agar 20.0 g/l Preparation: Salt solution 1.0 g FeSO4 x 7 H2O 1.0 g MnCl2 x 4 H2O 1.0 g ZNSO4 x 7 H2O in 100 ml water Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.2 Usage: Maintenance and taxonomy Organisms: All Actinomycetes
19535ISP 6yesName: ISP 6 (5318) Composition Peptone 15.0 g/l Proteose peptose 5.0 g/l Ferric ammonium citrate 0.5 g/l Sodium glycerophosphate 1.0 g/l Sodium thiosulfate 0.08 g/l Yeast extract 1.0 g/l Agar 15.0 g/l Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigments Organisms: All Actinomycetes
19535ISP 7yesName: ISP 7 (5322) Composition Glycerol 15.0 g/l L-Tyrosine 0.5 g/l L-Asparagine 1.0 g/l K2HPO4 0.5 g/l NaCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Trace element solution 5343 1.0 ml/l Agar 20.0 Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.3 Usage: Production of melanoid pigments Organisms: All Actinomycetes
41902MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
121294CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
19535positiveoptimum28mesophilic
191positivegrowth30mesophilic
41902positivegrowth30mesophilic
67770positivegrowth30mesophilic
121294positivegrowth25-45
121294nogrowth10psychrophilic
121294nogrowth15psychrophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 121294
  • oxygen tolerance: facultative anaerobe

compound production

  • @ref: 191
  • compound: nicotine blue

halophily

@refsaltgrowthtested relationconcentration
19535NaClpositivemaximum5 %
121294NaClpositivegrowth0-10 %

murein

  • @ref: 191
  • murein short key: A11.17
  • type: A3alpha L-Lys-L-Ala-L-Thr-L-Ala

observation

  • @ref: 67770
  • observation: quinones: MK-9(H2)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1953517234glucose+
1953522599arabinose+
1953517992sucrose+
1953518222xylose-
1953517268myo-inositol+
1953529864mannitol+
1953528757fructose+
1953526546rhamnose+
1953516634raffinose+
1953562968cellulose-
683685291gelatin+hydrolysis
6836827897tryptophan-energy source
6836816199urea+hydrolysis
6836816947citrate+assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis
12129416947citrate-carbon source
1212944853esculin-hydrolysis
121294606565hippurate+hydrolysis
12129417632nitrate+reduction
12129416301nitrite-reduction
12129435020tributyrin+hydrolysis
12129417632nitrate+respiration
6837917632nitrate+reduction
683794853esculin-hydrolysis
6837916199urea+hydrolysis
683795291gelatin+hydrolysis
6837917634D-glucose+fermentation
6837916988D-ribose+fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol+fermentation
6837917306maltose+fermentation
6837917716lactose+fermentation
6837917992sucrose+fermentation
6837928087glycogen+fermentation

antibiotic resistance

  • @ref: 121294
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

@refChebi-IDmetaboliteproduction
6836835581indoleno
6836816136hydrogen sulfideno
12129435581indoleno

metabolite tests

@refChebi-IDmetaboliteindole testvoges-proskauer-testmethylred-test
6836835581indole-
12129415688acetoin+
12129417234glucose+

enzymes

@refvalueactivityec
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
68379gelatinase+
68379urease+3.5.1.5
68379beta-glucosidase-3.2.1.21
68379N-acetyl-beta-glucosaminidase+3.2.1.52
68379alpha-glucosidase+3.2.1.20
68379beta-galactosidase+3.2.1.23
68379beta-glucuronidase+3.2.1.31
68379alkaline phosphatase-3.1.3.1
68379pyrrolidonyl arylamidase+3.4.19.3
68379pyrazinamidase+3.5.1.B15
68368gelatinase+
68368tryptophan deaminase-4.1.99.1
68368urease+3.5.1.5
68368ornithine decarboxylase-4.1.1.17
68368lysine decarboxylase-4.1.1.18
68368arginine dihydrolase-3.5.3.6
68368beta-galactosidase+3.2.1.23
121294oxidase-
121294beta-galactosidase+3.2.1.23
121294alcohol dehydrogenase-1.1.1.1
121294gelatinase+
121294amylase-
121294DNase-
121294caseinase-3.4.21.50
121294catalase+1.11.1.6
121294tween esterase-
121294gamma-glutamyltransferase-2.3.2.2
121294lecithinase+
121294lipase+
121294lysine decarboxylase-4.1.1.18
121294ornithine decarboxylase-4.1.1.17
121294phenylalanine ammonia-lyase+4.3.1.24
121294protease+
121294tryptophan deaminase-
121294urease-3.5.1.5

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
19535+++-++++-++++-+++++

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
19535+++-++++-++++-+++++
121294+++------+----+-----

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDGEL
19535+---+-+--+

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
121294++++---+-+++++--+--------+----++-+-+---+++-+-+------+------+++-++--+++--++++---+-----------+++-+-+-

Isolation, sampling and environmental information

taxonmaps

  • @ref: 69479
  • File name: preview.99_1652.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_99;97_106;98_115;99_1652&stattab=map
  • Last taxonomy: Paenarthrobacter
  • 16S sequence: X80743
  • Sequence Identity:
  • Total samples: 570
  • soil counts: 296
  • aquatic counts: 27
  • animal counts: 173
  • plant counts: 74

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
1911Risk group (German classification)
195351Hazard group
1212941Risk group (French classification)

Sequence information

16S sequences

  • @ref: 20218
  • description: A.nicotinovorans 16S rDNA
  • accession: X80743
  • length: 1468
  • database: ena
  • NCBI tax ID: 29320

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Paenarthrobacter nicotinovorans DSM 420GCA_017876445contigncbi29320
66792Paenarthrobacter nicotinovorans JCM 3874GCA_014648735scaffoldncbi29320
66792Paenarthrobacter nicotinovorans strain ATCC 4991929320.7plasmidpatric29320
66792Paenarthrobacter nicotinovorans strain DSM 42029320.24wgspatric29320
66792Paenarthrobacter nicotinovorans strain JCM 387429320.11wgspatric29320
66792Paenarthrobacter nicotinovorans DSM 4202918346339draftimg29320
66792Paenarthrobacter nicotinovorans ATCC 49919GCA_021919345completencbi29320

GC content

@refGC-contentmethod
19162.0high performance liquid chromatography (HPLC)
6777062.4high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedno96.81no
gram-positiveyes92.855no
anaerobicno99.632no
aerobicyes96.3no
halophileno94.485no
spore-formingno82.892no
motileno91.874no
glucose-fermentno82.964no
thermophileno99.076no
glucose-utilyes85.701yes

External links

@ref: 191

culture collection no.: DSM 420, ATCC 49919, JCM 3874, CGMCC 1.1933, CIP 106990, IAM 14587, IFO 15511, KCTC 9902, LMG 16253, NBRC 15511, NCAIM B.02133, NCAIM B.02288, VKM Ac-1988

straininfo link

  • @ref: 77021
  • straininfo: 10200

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny1581183Reclassification of two strains of Arthrobacter oxydans and proposal of Arthrobacter nicotinovorans sp. nov.Kodama Y, Yamamoto H, Amano N, Amachi TInt J Syst Bacteriol10.1099/00207713-42-2-2341992Amino Acid Sequence, Arthrobacter/*classification/genetics/ultrastructure, Chromatography, DNA, Bacterial, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistryGenetics
Metabolism15699198Identification of large linear plasmids in Arthrobacter spp. encoding the degradation of quinaldine to anthranilate.Overhage J, Sielker S, Homburg S, Parschat K, Fetzner SMicrobiology (Reading)10.1099/mic.0.27521-02005Amidohydrolases/genetics/metabolism, Arthrobacter/classification/*enzymology/genetics/growth & development, Biodegradation, Environmental, Conjugation, Genetic, Electrophoresis, Gel, Pulsed-Field, Metalloproteins/genetics/metabolism, Molecular Sequence Data, Oxidoreductases/genetics/metabolism, Plasmids/*genetics, Quinaldines/chemistry/*metabolism, Sequence Analysis, DNA, ortho-Aminobenzoates/chemistry/*metabolismEnzymology
Phylogeny24925596Arthrobacter bambusae sp. nov., isolated from soil of a bamboo grove.Park Y, Kook M, Ngo HTT, Kim KY, Park SY, Mavlonov GT, Yi THInt J Syst Evol Microbiol10.1099/ijs.0.064550-02014Arthrobacter/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Bambusa/*microbiology, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryGenetics
Genetics35536014Complete Genome Sequences of Two Closely Related Paenarthrobacter nicotinovorans Strains.El-Sabeh A, Honceriu I, Kallabi F, Boiangiu RS, Mihasan MMicrobiol Resour Announc10.1128/mra.00133-222022

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
191Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 420)https://www.dsmz.de/collection/catalogue/details/culture/DSM-420
19535Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM420.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
41902Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/19181
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68368Automatically annotated from API 20E
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
69479João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.https://microbeatlas.org/MicrobeAtlas 1.0 beta
77021Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID10200.1StrainInfo: A central database for resolving microbial strain identifiers
121294Curators of the CIPCollection of Institut Pasteur (CIP 106990)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106990